Darwins Frog Monomorphic Call Structure And Dimorphic vocal phenology

Preliminaries:

library(tidyverse)
library(ggplot2)  #  pretty plots
library(dplyr)  # dataframe manipulations and  %>% 
library(infer)  #  statistics
library(tidyr)  # nice tables that look nice
library(car)  # ANOVA 
library(formatR)  #to format R
library(knitr)  # inserting images
library(kableExtra)  # modifying kable tables
library(MASS)  # reported used for normalizing data for ANOVA

introduction:

[Include a brief summary of the paper you are reanalyzing data from (e.g., the overall objective of the paper, the types of data collected and how sampling was done, what the main results were) and lay out what you intend to replicate.]

background

The southern Darwin’s frog (Rhinoderma darwinii) mouth-brooding frog species endemic to Chilean Patagonia. R. darwinii has a fascinating method for reproduction: the female (egg-producer) deposits eggs and the male (sperm-producer) fertilizes them, then guards them until the embryos are visibly wriggling inside. Then the male transfers those eggs to their vocal sac where they will be safe from predators and receive nutrients from the male (similar to marsupial embryonic development in their pouch). Ultimately, the male broods these fertilized eggs, often from multiple clutches with different partners, in their vocal sacs for about 50 days, until fully developed froglets emerge by pushing their way out the male’s mouth! All a while during this gestation period, the male continues to call for mates (Sandmeier, 2016)! There are 3 sex roles in this species: pregnant male (MP), non-pregnant male (M or NPM), and female (H or F), and the main sexually dimporphic characteristic is size, where the egg-producers are slightly larger. In this nearly sexually monomorphic (i.e., the sexes look physically identical) species, mate selection depends on advertising calls, and R. darwinii is one of the few species where all sexes (PM, NPM, and F) use advertising calls to attract the attention of a potential mate (Serrano et al., 2020).

hypothesis

To address the gap in the literature regarding the calling behaviors of female R. darwinii, Serrano et al. (2020) hypothesized the time fluctuation of the each sex experiencing intasexual competition dictates the species position on the continuum of sexual monomorphism to dimorphism.

[the position along the monomorphism-dimorphism continuum of sexual signals depends on the time fluctuation of the sex experiencing intrasexual competition]

methods

They investigated this with a population of southern R. darwinii on Chiolé Island in Southern Chile during mating season (October 2015-February 2016). In the field, they first recorded individual calls (tracks) then collected population monitoring data (snout-vent length (mm), SVL; weight (g); internal temperature(ºC)). They also collected data on the sex and sexual status (MP = pregnant male, H = female, M = non-pregnant male) of each frog caught using body size and morphological characteristics. For the pregnant males, they counted externally the number of larvae in the vocal sacs. For each call recordings, they measured the call repetition rate (number of calls made in a 5 min period), the sound pressure level (SPL, dB), call duration (CD, seconds), the number of notes per call (NC), the note duration (ND, ms), the dominant frequency of the call (DF, Hz); and the amplitude of each vocalization (root mean square (RMS) amplitude).

results

data replication

lay out what you intend to replicate.

Visualization of Data

[Include a view of the first few lines of the dataset plus any exploratory data analysis - e.g., overview of descriptive statistics included in the paper, plots, etc.]

load in dataset:

f <- "https://raw.githubusercontent.com/slcornett/data-analysis-replication/main/data/Serrano_et_al_2020_MPMH.csv"
d <- read_csv(f, col_names = TRUE, show_col_types = FALSE) # show column names, hides dataframe message details
kable(head(d), align = 'l', booktabs = TRUE) %>% # to make a table, left aligned data, output of head(d)
  kable_styling(font_size = 9) # specifying font size
Nombre Captura Sex Sexo Track Calls5min Temp HR Larvas LHC Peso SPL NC ND CD Agg Entropy Avg Entropy DF RMS Amp
Eugenia 142 Females H 376L 8 NA NA NA 23.4 1.15 71.43103 15 0.2565455 2.141000 1.379379 1.524621 3340.876 162764.3
Michelle 158 Non-pregnant males M 162L 4 15.4 84.2 NA 22.4 NA 63.22143 17 0.1556250 1.557000 2.427146 2.031938 3402.231 89155.9
Dr<e1>cula 171 Females H 172R 5 NA NA NA 23.7 1.10 NA 12 0.1964600 2.008200 1.959700 1.851720 3686.474 53409.7
Herlinda 173 Non-pregnant males M 171L 5 NA NA NA 22.7 0.92 62.77895 33 0.1815974 1.723222 2.882636 2.690169 3487.814 110800.1
Luisa 175 Females H 179L 11 NA NA NA 23.2 1.06 64.16923 14 0.1571250 NA 1.926542 1.766208 3682.167 43954.0
Femalesrancisco 176 Pregnant males MP 174L 3 NA NA 5 22.6 1.11 62.37500 14 0.1764444 1.737125 2.544982 2.458500 3633.539 62616.0

• DESCRIPTIONS/IDENTIFIERS:
- Nombre = name given to ID the frog;
- Captura = number captured/image name;
- Track = the call recording track

• PHYSICAL MEASUREMENTS:
- sexo = sexual status (MP = pregnant male, H = female, M = non-pregnant male)
- peso = mass (g);
- LHC = longitud hocico a cola (snout-vent length, mm);
- temp = temperature (ºC);
- HR = relative humidity;
- larvas = number of tadpoles/offspring in their parent’s mouth!

• ACOUSTIC VARIABLES:
- Calls5min = calls in 5 min interval (call repetition rate);  - SPL = Sound Pressure Level (dB);  - NC = number of notes/call;
- ND = note duration (ms);
- CD = call duration (s);
- Agg Entropy = aggregate entropy;
- Avg Entropy = average entropy;  - DF = dominant frequency of call (Hz);
- RMS Amp = Root Mean Square Amplitude

Statistical Replications/Reanalysis

[Be sure to thoroughly explain what replications you are doing and comment your code so that it is easy for a reader to understand. Include in this section relevant tables/figures/values from the original paper for comparison to what you accomplished with your replication. Note that I want you to do the bulk of any exposition using text and markdown syntax outside of code blocks. That is, your document should not just be one big code block with R style comments but rather a nicely formatted report with code separated from exposition, interpretation, and dicussion.]

Summary/Discussion

Narrative section that overviews how successful were you at replicating the analyses and visualizations in the study.
1. What problems did you encounter?
2. Why might you have encountered those problems?
3. What details were lacking from the original study’s methods that might have hampered your ability to replicate the authors’ results?

References

[Include the citation for your paper, plus any other literature you might reference.] Sandmeier, F. (2016). Rhinoderma darwinii [Encyclopedia]. AmphibiaWeb; University of California, Berkeley, CA, USA. https://amphibiaweb.org/species/4322

Serrano, J. M., Penna, M., Valenzuela-Sánchez, A., Mendez, M. A., & Azat, C. (2020). Monomorphic call structure and dimorphic vocal phenology in a sex-role reversed frog. Behavioral Ecology and Sociobiology, 74(10), 127. https://doi.org/10.1007/s00265-020-02903-3